Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana
Abstract Background C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at genome-wide level, the cis and trans determinants affecting the occurrence...
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| Format: | Article |
| Language: | English |
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BMC
2020-09-01
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| Series: | BMC Genetics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12863-020-00907-6 |
| _version_ | 1811302546014208000 |
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| author | Duan Chu Lai Wei |
| author_facet | Duan Chu Lai Wei |
| author_sort | Duan Chu |
| collection | DOAJ |
| description | Abstract Background C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at genome-wide level, the cis and trans determinants affecting the occurrence or editing levels of these C-to-U events are relatively less studied. What is known is that the PPR (pentatricopeptide repeat) proteins are the main trans-regulatory elements responsible for the C-to-U conversion, but other determinants especially the cis-regulatory elements remain largely uninvestigated. Results By analyzing the transcriptome and translatome data in Arabidopsis thaliana roots and shoots, combined with RNA-seq data from hybrids of Arabidopsis thaliana and Arabidopsis lyrata, we perform genome-wide investigation on the cis elements and trans-regulatory elements that potentially affect C-to-U editing events. An upstream guanosine or double-stranded RNA (dsRNA) regions are unfavorable for editing events. Meanwhile, many genes including the transcription factors may indirectly play regulatory roles in trans. Conclusions The 5-prime thymidine facilitates editing and dsRNA structures prevent editing in cis. Many transcription factors affect editing in trans. Although the detailed molecular mechanisms underlying the cis and trans regulation remain to be experimentally verified, our findings provide novel aspects in studying the botanical C-to-U RNA editing events. |
| first_indexed | 2024-04-13T07:29:57Z |
| format | Article |
| id | doaj.art-2790f7bbf7bd4e429806f19d0b82aa77 |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-13T07:29:57Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-2790f7bbf7bd4e429806f19d0b82aa772022-12-22T02:56:22ZengBMCBMC Genetics1471-21562020-09-0121111010.1186/s12863-020-00907-6Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thalianaDuan Chu0Lai Wei1College of Life Sciences, Beijing Normal UniversityCollege of Life Sciences, Beijing Normal UniversityAbstract Background C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at genome-wide level, the cis and trans determinants affecting the occurrence or editing levels of these C-to-U events are relatively less studied. What is known is that the PPR (pentatricopeptide repeat) proteins are the main trans-regulatory elements responsible for the C-to-U conversion, but other determinants especially the cis-regulatory elements remain largely uninvestigated. Results By analyzing the transcriptome and translatome data in Arabidopsis thaliana roots and shoots, combined with RNA-seq data from hybrids of Arabidopsis thaliana and Arabidopsis lyrata, we perform genome-wide investigation on the cis elements and trans-regulatory elements that potentially affect C-to-U editing events. An upstream guanosine or double-stranded RNA (dsRNA) regions are unfavorable for editing events. Meanwhile, many genes including the transcription factors may indirectly play regulatory roles in trans. Conclusions The 5-prime thymidine facilitates editing and dsRNA structures prevent editing in cis. Many transcription factors affect editing in trans. Although the detailed molecular mechanisms underlying the cis and trans regulation remain to be experimentally verified, our findings provide novel aspects in studying the botanical C-to-U RNA editing events.http://link.springer.com/article/10.1186/s12863-020-00907-6C-to-U RNA editingCisTransRegulatoryArabidopsisSynonyms“Missense” and “nonsynonymous”. |
| spellingShingle | Duan Chu Lai Wei Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana BMC Genetics C-to-U RNA editing Cis Trans Regulatory Arabidopsis Synonyms“Missense” and “nonsynonymous”. |
| title | Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana |
| title_full | Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana |
| title_fullStr | Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana |
| title_full_unstemmed | Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana |
| title_short | Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana |
| title_sort | systematic analysis reveals cis and trans determinants affecting c to u rna editing in arabidopsis thaliana |
| topic | C-to-U RNA editing Cis Trans Regulatory Arabidopsis Synonyms“Missense” and “nonsynonymous”. |
| url | http://link.springer.com/article/10.1186/s12863-020-00907-6 |
| work_keys_str_mv | AT duanchu systematicanalysisrevealscisandtransdeterminantsaffectingctournaeditinginarabidopsisthaliana AT laiwei systematicanalysisrevealscisandtransdeterminantsaffectingctournaeditinginarabidopsisthaliana |